genome.fa.s1.2.7.7.80.10.50.1000.14.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   

This is table  14  of  187  ( 22383 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5087588--5087622	18	1.9	18	100	0	70	34	0	14	51	1.42
5087629--5087753	59	2.1	59	85	5	164	32	3	1	62	1.21
5088584--5088709	9	13.8	9	69	17	64	58	3	0	36	1.22
5088581--5088639	29	2.0	29	83	6	75	61	3	1	33	1.23
5088632--5088706	19	4.3	17	71	17	57	58	4	0	37	1.17
5093482--5093518	19	1.9	19	94	0	65	32	0	2	64	1.07
5093461--5093566	50	2.1	50	87	3	151	27	0	15	56	1.45
5099743--5099793	23	2.2	23	82	0	66	49	0	3	47	1.20
5099983--5100015	16	2.1	16	94	0	57	36	3	3	57	1.29
5106823--5106849	4	6.8	4	100	0	54	48	0	0	51	1.00
5107091--5107150	24	2.5	23	76	7	57	30	20	1	48	1.59
5116840--5117138	50	5.8	50	90	2	409	21	31	22	25	1.98
5118355--5118418	26	2.5	26	94	0	110	9	32	3	54	1.48
5118367--5118412	14	3.4	14	70	11	51	8	30	4	56	1.49
5121739--5121811	29	2.5	29	90	0	119	46	13	9	30	1.75
5127150--5127212	11	5.8	11	80	7	67	12	6	3	77	1.07
5127147--5127184	19	2.0	19	85	10	51	13	7	2	76	1.11
5128396--5128468	29	2.5	29	88	0	110	47	13	8	30	1.72
5128987--5129011	11	2.3	11	100	0	50	24	8	12	56	1.62
5129639--5129681	20	2.2	20	87	8	61	65	0	4	30	1.13
5129980--5130015	2	18.0	2	100	0	72	50	0	0	50	1.00
5135532--5135596	33	1.9	34	84	9	89	46	3	3	47	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5135621--5135662	22	2.0	22	95	4	77	47	4	4	42	1.45
5135766--5135833	23	3.0	23	82	4	75	48	1	2	47	1.26
5135967--5136007	14	2.8	15	85	7	57	56	0	4	39	1.21
5135990--5136061	33	2.2	34	80	12	87	55	11	6	26	1.60
5136054--5136101	20	2.4	20	86	13	64	50	8	4	37	1.52
5136824--5136873	25	2.0	25	92	0	82	8	28	4	60	1.43
5139501--5139539	20	2.0	20	94	0	69	48	0	2	48	1.15
5139560--5139646	33	2.7	33	78	1	95	47	16	9	27	1.76
5139626--5139691	34	1.9	34	87	6	98	48	13	6	31	1.67
5139661--5139700	14	2.9	15	85	10	50	47	15	2	35	1.58
5144178--5144202	12	2.1	12	100	0	50	36	16	8	40	1.77
5144557--5144734	93	1.9	93	82	4	225	45	11	12	29	1.78
5144688--5144775	45	2.0	45	83	0	113	45	11	19	23	1.83
5148851--5148907	30	1.9	30	82	7	71	43	5	12	38	1.65
5151168--5151224	30	1.9	30	85	0	78	57	0	5	36	1.21
5158892--5158918	11	2.5	11	100	0	54	14	0	7	77	0.97
5159803--5159832	16	1.9	16	93	6	53	40	6	3	50	1.45
5166951--5166990	11	3.5	11	80	6	53	35	7	22	35	1.82
5167510--5167541	10	3.1	10	91	8	55	0	9	0	90	0.45
5167510--5167541	11	3.0	11	95	4	57	0	9	0	90	0.45
5168082--5168279	99	2.0	99	88	0	297	35	12	15	36	1.85
5169022--5169079	30	1.9	30	85	0	80	48	13	5	32	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5178213--5178268	26	2.2	25	81	9	60	58	21	1	17	1.47
5178708--5178754	2	23.5	2	95	0	85	0	46	0	53	1.00
5192367--5192419	27	2.0	27	85	7	74	28	0	1	69	0.99
5193301--5193395	48	2.0	48	100	0	190	33	12	16	36	1.87
5193349--5193734	91	4.2	90	85	3	434	34	18	17	29	1.94
5193210--5193486	139	2.0	139	90	1	439	34	16	17	31	1.92
5193647--5194979	122	10.9	122	86	2	1757	33	17	18	30	1.94
5193647--5194977	486	2.7	484	85	3	1747	33	17	18	30	1.94
5197211--5197251	21	2.0	21	85	9	57	46	2	0	51	1.14
5199274--5199525	126	2.0	124	92	1	414	40	17	9	32	1.82
5200727--5200776	19	2.5	20	81	15	68	40	2	6	52	1.38
5210054--5210094	18	2.2	19	86	4	57	46	0	7	46	1.30
5210469--5211047	155	3.8	151	84	6	749	52	8	9	30	1.63
5210716--5210767	13	4.0	13	75	9	52	65	7	1	25	1.30
5210460--5211047	153	3.9	152	83	7	755	51	8	9	30	1.63
5211102--5211154	19	3.0	17	78	10	61	35	9	18	35	1.84
5211126--5211170	23	2.0	23	91	4	74	37	4	17	40	1.70
5211136--5211180	23	2.0	23	86	4	65	33	4	15	46	1.66
5211595--5211634	3	13.3	3	84	10	55	32	0	0	67	0.91
5211579--5211633	15	3.7	15	74	16	53	30	0	1	67	1.01
5211581--5211632	12	4.1	12	80	14	52	28	0	1	69	0.99
5211903--5212002	52	1.9	52	84	6	132	31	6	7	56	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5212994--5213359	153	2.4	152	88	6	542	52	8	11	28	1.66
5213432--5213551	61	2.0	61	80	4	136	22	3	11	62	1.43
5221625--5221663	21	2.0	20	85	10	53	66	2	0	30	1.05
5225015--5225063	2	24.5	2	100	0	98	51	0	0	48	1.00
5228629--5228683	26	2.1	27	82	3	67	49	5	0	45	1.25
5242175--5242216	21	2.0	21	85	0	57	42	7	7	42	1.59
5247856--5247896	20	2.1	19	86	4	55	48	2	2	46	1.28
5261713--5261764	20	2.6	21	84	6	72	46	0	0	53	1.00
5261711--5261763	18	2.8	19	82	5	63	45	0	0	54	0.99
5264513--5264681	68	2.5	68	91	0	266	40	14	21	23	1.90
5270101--5270221	42	3.0	40	74	17	122	56	3	4	35	1.38
5271897--5271951	19	2.9	19	81	2	67	27	29	27	16	1.97
5272404--5272430	11	2.5	11	100	0	54	29	7	7	55	1.55
5274728--5274792	27	2.4	27	81	0	94	26	33	32	7	1.85
5274868--5274958	6	15.3	6	80	13	57	56	0	42	1	1.06
5274893--5274929	3	11.7	3	88	11	56	62	0	37	0	0.96
5274889--5274943	7	8.4	7	88	6	64	56	0	41	1	1.10
5274868--5274929	29	2.1	29	82	11	74	61	0	38	0	0.96
5275181--5275258	38	2.1	38	88	4	115	30	1	12	55	1.46
5276929--5276987	25	2.3	25	82	8	66	59	10	5	25	1.50
5279063--5279751	160	4.3	159	91	3	1100	29	7	9	53	1.62
5279063--5279751	319	2.2	318	91	3	1109	29	7	9	53	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5279763--5279810	14	3.2	15	73	8	53	16	8	6	68	1.35
5279912--5280022	30	4.0	30	76	17	139	60	9	6	24	1.50
5279898--5279966	14	4.8	14	75	16	61	68	5	2	23	1.25
5279908--5280008	52	1.9	52	93	0	175	62	7	4	24	1.43
5279964--5280034	30	2.4	30	88	4	99	60	9	7	22	1.52
5279900--5280076	82	2.2	81	75	11	175	61	6	6	25	1.45
5280268--5280380	3	39.0	3	72	13	76	0	37	1	61	1.07
5280335--5280377	5	8.2	5	87	7	59	0	34	0	65	0.93
5281153--5281180	2	14.0	2	100	0	56	50	0	0	50	1.00
5281397--5281437	21	1.9	22	90	5	66	65	2	0	31	1.05
5281397--5281442	21	2.2	21	84	7	58	69	2	0	28	1.00
5289892--5289956	30	2.3	29	87	12	93	43	9	0	47	1.35
5290024--5290115	27	3.4	27	89	0	139	28	27	29	15	1.96
5290196--5290233	11	3.5	11	85	7	60	71	0	28	0	0.87
5290195--5290233	21	1.9	20	94	5	69	69	0	30	0	0.89
5290359--5290393	3	11.7	3	100	0	70	31	0	0	68	0.90
5290392--5290426	3	11.7	3	100	0	70	0	0	31	68	0.90
5292766--5292933	51	3.3	52	74	16	147	0	33	0	66	0.97
5292814--5292891	10	8.1	10	69	18	58	0	29	0	70	0.87
5292824--5292934	4	27.0	4	78	18	70	0	33	0	66	0.92
5292801--5292873	36	1.9	39	86	13	109	0	32	0	67	0.91
5292804--5292934	44	3.0	43	78	16	137	0	34	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5292767--5292891	57	2.3	55	86	9	166	0	31	0	68	0.96
5292784--5292930	57	2.6	57	78	12	158	0	36	0	63	1.00
5293192--5293248	16	3.6	16	95	0	87	29	0	36	33	1.58
5293483--5293617	15	8.9	15	65	24	61	50	3	2	43	1.32
5293543--5293633	44	2.1	43	81	6	103	53	3	2	40	1.29
5293702--5293737	17	2.2	16	86	13	56	47	0	5	47	1.25
5293706--5293751	17	2.5	20	86	13	71	45	2	6	45	1.41
5293758--5293951	93	2.1	91	88	3	282	47	4	4	43	1.41
5293808--5293944	47	2.9	47	70	14	122	47	5	3	43	1.43
5301371--5301547	77	2.3	77	88	2	257	38	8	20	32	1.83

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187